It might be. What operating system are you on? What's your application written in?
At the moment I'm using OS X. My application uses Tod's arduino-serial (http://todbot.com/blog/2006/12/06/arduino-serial-c-code-to-talk-to-arduino/
) to send information to the Arduino from a simple perl script. (The perl script SSHes into a remote server and gathers some stats to display on the Arduino.)
Can you simply keep the serial connection open the whole time?
Keeping a serial connection constantly open is one possible workaround, but I was wondering if there's a way to temporarily disable the Arduino's software reset so that I would not have to have keep the serial connection open.